INCLUSive: INtegrated Clustering, Upstream sequence retrieval and motif Sampling

Keywords

Cluster analysis, Sequence motif, Motif (music), Computer science, Sampling (signal processing)

References

• Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.Charles E. Lawrence, Stephen F. Altschul, Mark S. Boguski — 1993
• A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed GenesGert Thijs, Kathleen Marchal, Magali Lescot — 2001
• Database resources of the National Center for Biotechnology Information: updateDavid Wheeler — 2004
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.Stephen F. Altschul — 1997
• A higher-order background model improves the detection of promoter regulatory elements by Gibbs samplingGert Thijs, Magali Lescot, Kathleen Marchal — 2001
• Adaptive quality-based clustering of gene expression profilesFrank De Smet, Janick Mathys, Kathleen Marchal — 2002
• APPLICATION NOTED. Bassoni, Ph. Elizabeth Quinn, M. Pratap — 1997

Cited by

• MARAN: Normalizing Micro-array Data井阪直樹 — 2003
• Dynamique des hélitrons dans le genome d'Arabidopsis thaliana : développement de nouvelles stratégies d'analyse des éléments transposables. (Dynamics of transposable elements in the genome of Arabidopsis thaliana: development of new strategies for the analysis of transposable elements)Sébastien Tempel — 2007
• A systems biology design and implementation of novel bioinformatics software tools for high throughput gene expression analysisMohsin Amir Faiz Khan — 2009
• Early hypoxia-regulated genes in rice and Arabidopsis thalianaMathias Klode — 2011
• Integrating quality-based clustering of microarray data with Gibbs sampling for the discovery of regulatory motifsYves Moreau, Gert Thijs, Kathleen Marchal — 2002
• In silico identification of metazoan transcriptional regulatory regionsWyeth W. Wasserman, William Krivan — 2003
• A data integration framework for prediction of transcription factor targets: a BCL6 case studyMatti Nykter, Harri Lähdesmäki, Alistair G. Rust — 2009
• Soybean (Glycine max) SWEET gene family: insights through comparative genomics, transcriptome profiling and whole genome re-sequence analysisGunvant Patil, Babu Valliyodan, Rupesh Deshmukh — 2015
• The Effect of Orthology and Coregulation on Detecting Regulatory MotifsValérie Storms, Marleen Claeys, Aminael Sánchez — 2010
• Increasing Coverage of Transcription Factor Position Weight Matrices through Domain-level HomologyBrady Bernard, Vésteinn Thórsson, Hector Rovira — 2012
• Computational Approaches to Identify Promoters and cis-Regulatory Elements in Plant Genomes1Stéphane Rombauts, Kobe Florquin, Magali Lescot — 2003
• Delineation of the Salmonella enterica Serovar Typhimurium HilA Regulon through Genome-Wide Location and Transcript AnalysisInge M Thijs, Sigrid C. J. De Keersmaecker, Abeer Fadda — 2007
• Tissue-specific regulatory network extractor (TS-REX): a database and software resource for the tissue and cell type-specific investigation of transcription factor-gene networksF. Colecchia, Denise Kottwitz, Mandy Wagner — 2009
• INCLUSive: a web portal and service registry for microarray and regulatory sequence analysisBert Coessens — 2003
• Rhodobase, a meta-analytical tool for reconstructing gene regulatory networks in a model photosynthetic bacteriumOleg V. Moskvin, Dmitriy A. Bolotin, Andrew Wang — 2011
• Bioinformatics: Organisms from Venus, Technology from Jupiter, Algorithms from MarsBart De Moor, Kathleen Marchal, Janick Mathys — 2003
• MotifCluster: an interactive online tool for clustering and visualizing sequences using shared motifsMicah Hamady, Jeremy Widmann, Shelley D. Copley — 2008
• A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulationNathaniel R. Street, Stefan Jansson, Torgeir R. Hvidsten — 2011
• PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequencesMagali Lescot — 2002
• Role of the transcription factor C/EBPδ in a regulatory circuit that discriminates between transient and persistent Toll-like receptor 4-induced signalsVladimir Litvak, Stephen A. Ramsey, Alistair G. Rust — 2009

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